Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-11-30

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All times shown according to UTC.

Time Nick Message
00:06 carandraug left #bioperl
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02:04 piotr hello
02:05 piotr is anyone here?
02:05 deafferret piotr: hola
02:06 piotr i am looking into learning to use perl to analyze genomic data
02:07 piotr can anyone point me to a resource that could help me with this?
02:08 piotr i have no understanding at this point on how to access and extract data from the ncbi and other databases and analyze them
02:09 rbuels piotr: try starting with the bioperl how-to documents: http://www.bioperl.org/wiki/HOWTOs
02:09 piotr is perl the ebst language to learn for such purpose?
02:09 piotr i have some basic konwledge of c++
02:10 piotr thanks for the link, seems very good
02:11 deafferret to my knowledge BioPerl is the most complete Bio* project
02:15 piotr does bioperl offer complete programs?
02:16 deafferret the scripts/ directory has a bunch I believe
02:16 rbuels piotr: there are some complete programs as part of bioperl, yes.  but bioperl is mainly a toolkit for building your own programs.
02:17 piotr what do you mean
02:17 piotr what are the tools?
02:18 piotr are those the modules?
02:18 deafferret why don't you start with whatever you're trying to accomplish and explore from there?
02:21 piotr yeah sorry for the dumb questions
02:21 piotr i am trying to get a hold on what perl does
02:21 piotr i will read the material online
02:24 rbuels piotr: perl is a programming language.  like C.
02:24 rbuels piotr: you write programs in it.
02:24 rbuels piotr: BioPerl is a toolkit you can use in the programs you write.
02:25 piotr can u give me an example
02:25 piotr of a tool u can use from bioperl
02:26 rbuels piotr: you can fetch sequences from NCBI, and then run BLAST on them.
02:26 rbuels piotr: with bioperl tools.
02:26 rbuels for example
02:26 piotr cool, so the code for that is already written and shared for everyone to use
02:27 rbuels piotr: yes, the bioperl toolkit has code for making it much easier to do that
02:27 piotr great
02:32 piotr what's the best way to elarn to program in perl?
02:32 piotr just go through the tutorials and try to write little programs?
02:32 deafferret I like "learning Perl" by O'Reilly.   and/or learn.perl.org
02:33 piotr do i need any prior knowledge on top of basic, at this point, conceptual knowledge of c++
02:34 piotr do i need to know how to use unix? the terminal on the mac?
02:34 piotr I had a very hard time, still unsuccessful in installing Perl on a mac
02:34 deafferret ?   perl is pre-installed in OS X. that's what I use (and Linux)
02:35 piotr so u use terminal to run perl programs that u write in notepad?
02:35 piotr i am used to using a compiler for C++ that let's u do everything from within itself
02:36 piotr is there something user fridnly like that to prograsm in perl?
02:37 deafferret you can use whatever text editor you like. I use vi.
02:38 piotr and then, do u run them in terminal?
02:39 deafferret notepad or Komodo or TextMate or Eclipse or whatever
02:39 deafferret I run vi in Terminal.app, yes.
02:39 deafferret then    perl myprogram.pl
02:39 deafferret or stick   #!/usr/bin/perl    at the top of your program
02:40 piotr cool
02:40 piotr i see i have a lot to learm
02:40 piotr thatnks for ur help
02:41 deafferret sure   :)
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